Package ‘AquaEnv’
September 6, 2016
Version 1.0-4
Title Integrated Development Toolbox for Aquatic Chemical Model
Generation
Author Andreas F. Hofmann, Karline Soetaert, Filip J.R. Meysman,
Mathilde Hagens
Maintainer Karline Soetaert <[email protected]>
Depends R (>= 2.15.0)
Imports minpack.lm, graphics, grDevices, stats
Suggests deSolve
Description Toolbox for the experimental aquatic chemist, focused on
acidification and CO2 air-water exchange. It contains all elements to
model the pH, the related CO2 air-water exchange, and
aquatic acid-base chemistry for an arbitrary marine,
estuarine or freshwater system. It contains a suite of tools for
sensitivity analysis, visualisation, modelling of chemical batches,
and can be used to build dynamic models of aquatic systems.
As from version 1.0-4, it also contains functions to calculate
the buffer factors.
License GPL (>= 2)
LazyData yes
Repository CRAN
Date/Publication 2016-09-06 16:39:52
NeedsCompilation no
Repository/R-Forge/Project aquaenv
Repository/R-Forge/Revision 97
Repository/R-Forge/DateTimeStamp 2016-09-05 13:48:52
R topics documented:
aquaenv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
AquaEnv_package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
2
8
2
aquaenv
as.data.frame.aquaenv
BufferFactors . . . .
c.aquaenv . . . . . .
ConcRelCl . . . . . .
convert . . . . . . . .
DeltaPcoeffs . . . . .
gauge_p . . . . . . .
K0_CO2 . . . . . . .
K0_O2 . . . . . . . .
Ksp_aragonite . . . .
Ksp_calcite . . . . .
K_BOH3 . . . . . .
K_CO2 . . . . . . .
K_H2PO4 . . . . . .
K_H2S . . . . . . .
K_H3PO4 . . . . . .
K_HCO3 . . . . . .
K_HF . . . . . . . .
K_HPO4 . . . . . .
K_HSO4 . . . . . .
K_NH4 . . . . . . .
K_SiOH4 . . . . . .
K_SiOOH3 . . . . .
K_W . . . . . . . . .
length.aquaenv . . .
MeanMolecularMass
merge.aquaenv . . .
PhysChemConst . . .
plot.aquaenv . . . . .
sample_dickson1981
sample_dickson2007
TAfit . . . . . . . . .
Technicals . . . . . .
titration . . . . . . .
watdepth . . . . . . .
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Index
aquaenv
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aquaenv
Description
PUBLIC function: the main function of the package AquaEnv: creates an object of class aquaenv
aquaenv
3
Usage
aquaenv(S, t, p=pmax((P-Pa), gauge_p(d, lat, Pa)),
P=Pa, Pa=1.01325, d=0, lat=0,
SumCO2=0, SumNH4=0, SumH2S=0, SumH3PO4=0,
SumSiOH4=0, SumHNO3=0, SumHNO2=0, SumBOH3=NULL,
SumH2SO4=NULL, SumHF=NULL, TA=NULL, pH=NULL, fCO2=NULL, CO2=NULL,
speciation=TRUE, dsa=FALSE, ae=NULL, from.data.frame=FALSE,
SumH2SO4_Koffset=0, SumHF_Koffset=0, revelle=FALSE, skeleton=FALSE,
k_w=NULL, k_co2=NULL, k_hco3=NULL, k_boh3=NULL, k_hso4=NULL,
k_hf=NULL, k1k2="lueker", khf="dickson", khso4="dickson",
fCO2atm=0.000400, fO2atm=0.20946)
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars, standard is
calculated either from the given P, or the given d, lat, and Pa
P
total pressure in bars, standard: Pa (at the surface)
Pa
atmospheric pressure in bars, standard: 1 atm (at sea-level)
d
depth below the surface in meters, standard: 0 (at the surface)
lat
latitude in degrees (-90 to +90) to calculate the gravitational constant g for calculating the water depth from the pressure and vice versa, standard: 0
SumCO2
total carbonate concentration in mol/kg-solution, if NULL is supplied it is calculated
SumNH4
total ammonium concentration in mol/kg-solution, optional
SumH2S
total sulfide concentration in mol/kg-solution, optional
SumH3PO4
total phosphate concentration in mol/kg-solution, optional
SumSiOH4
total silicate concentration in mol/kg-solution, optional
SumHNO3
total nitrate concentration in mol/kg-solution, optional
SumHNO2
total nitrite concentration in mol/kg-solution, optional
SumBOH3
total borate concentration in mol/kg-solution, calculated from S if not supplied
SumH2SO4
total sulfate concentration in mol/kg-solution, calculated from S if not supplied
SumHF
total fluoride concentration in mol/kg-solution, calculated from S if not supplied
TA
total alkalinity in mol/kg-solution, if supplied, pH will be calculated
pH
pH on the free proton concentration scale, if supplied, total alkalinity will be
calculated
fCO2
fugacity of CO2 in the water in atm (i.e. the fugacity of CO2 in a small volume
of air fully equilibrated with a sufficiently large sample of water), can be used
with either [TA], pH, or [CO2] to define the system
CO2
concentration of CO2, can be used with either [TA], pH, or fCO2 to define the
system
4
aquaenv
speciation
dsa
ae
flag: TRUE = full speciation is calculated
flag: TRUE = all information necessary to build a pH model with the direct
substitution approach (DSA, Hofmann2008) is calculated
either an object of class aquaenv used for the cloning functionality or a dataframe
used for the from.data.frame functionality. Note that for cloning the desired
k1k2 and khf values need to be specified! (otherwise the default values are used
for the cloned object)
from.data.frame
flag: TRUE = the object of class aquaenv is built from the data frame supplied
in ae
SumH2SO4_Koffset
only used internally to calculate dTAdKdKdSumH2SO4
SumHF_Koffset only used internally to calculate dTAdKdKdSumHF
revelle
flag: TRUE = the revelle factor is numerically calculated. We do however
strongly encourage to use the analytical calculation from BufferFactors$RF
skeleton
flag: TRUE = a reduced amount of information is calculated yielding a smaller
object of type aquaenv
k_w
a fixed K\_W can be specified
k_co2
a fixed K\_CO2 can be specified; used for TA fitting: give a K\_CO2 and NOT
calculate it from T and S: i.e. K\_CO2 can be fitted in the routine as well
k_hco3
a fixed K\_HCO3 can be specified
k_boh3
a fixed K\_BOH3 can be specified
k_hso4
a fixed K\_HSO4 can be specified
k_hf
a fixed K\_HF can be specified
k1k2
either "lueker" (default, Lueker2000), "roy" (Roy1993a), or "millero" (Millero2006)
for K\_CO2 and K\_HCO3.
khf
either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) for K\_HF
khso4
either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) for K\_HSO4
fCO2atm
atmospheric fugacity of CO2 in atm, default = 0.000400 atm
fO2atm
atmospheric fugacity of O2 in atm, default = 0.20946 atm
Value
a list containing: "S" "t" "p" "T" "Cl" "I" "P" "Pa" "d" "density" "SumCO2" "SumNH4" "SumH2S"
"SumHNO3" "SumHNO2" "SumH3PO4" "SumSiOH4" "SumBOH3" "SumH2SO4" "SumHF" "Br"
"ClConc" "Na" "Mg" "Ca" "K" "Sr" "molal2molin" "free2tot" "free2sws" "tot2free" "tot2sws"
"sws2free" "sws2tot" "K0\_CO2" "K0\_O2" "fCO2atm" "fO2atm" "CO2\_sat" "O2\_sat" "K\_W"
"K\_HSO4" "K\_HF" "K\_CO2" "K\_HCO3" "K\_BOH3" "K\_NH4" "K\_H2S" "K\_H3PO4" "K\_H2PO4"
"K\_HPO4" "K\_SiOH4" "K\_SiOOH3" "K\_HNO2" "K\_HNO3" "K\_H2SO4" "K\_HS" "Ksp\_calcite"
"Ksp\_aragonite" "TA" "pH" "fCO2" "CO2" "HCO3" "CO3" "BOH3" "BOH4" "OH" "H3PO4"
"H2PO4" "HPO4" "PO4" "SiOH4" "SiOOH3" "SiO2OH2" "H2S" "HS" "S2min" "NH4" "NH3"
"H2SO4" "HSO4" "SO4" "HF" "F" "HNO3" "NO3" "HNO2" "NO2" "omega\_calcite" "omega\_aragonite"
"revelle" "c1" "c2" "c3" "dTAdSumCO2" "b1" "b2" "dTAdSumBOH3" "so1" "so2" "so3" "dTAdSumH2SO4"
"f1" "f2" "dTAdSumHF" "dTAdH" "dTAdKdKdS" "dTAdKdKdT" "dTAdKdKdd" "dTAdKdKdSumH2SO4" "dTAdKdKdSumHF" or a subset of this set. Please consult the vignette of AquaEnv
for more details
aquaenv
5
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Examples
## Not run:
############################
# Minimal aquaenv definition
############################
ae <- aquaenv(S=30, t=15)
ae$K_CO2
ae$Ksp_calcite
ae$Ksp_aragonite
ae <- aquaenv(S=30,
ae <- aquaenv(S=30,
ae <- aquaenv(S=30,
ae <- aquaenv(S=30,
ae$K_CO2
t=15,
t=15,
t=15,
t=15,
p=10)
P=11)
d=100)
d=100, Pa=0.5)
ae$Ksp_calcite
ae$Ksp_aragonite
ae
########################################################
# Defining the complete aquaenv system in different ways
########################################################
S
<- 30
t
<- 15
p
<- gauge_p(d=10) # ~ p <- 0.1*10*1.01325
SumCO2 <- 0.0020
pH
<- 8
TA
<- 0.002140798
fCO2
<- 0.0005326744
CO2
<- 2.051946e-05
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH)
ae$TA
ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA)
ae$pH
ae <- aquaenv(S, t, p, SumCO2=SumCO2, CO2=CO2)
ae$pH
ae <- aquaenv(S, t, p, SumCO2=SumCO2, fCO2=fCO2)
ae$pH
ae <- aquaenv(S, t, p, SumCO2=SumCO2, CO2=CO2, fCO2=fCO2)
6
aquaenv
ae
ae
ae
ae
ae
<<<<<-
aquaenv(S,
aquaenv(S,
aquaenv(S,
aquaenv(S,
aquaenv(S,
t,
t,
t,
t,
t,
p,
p,
p,
p,
p,
SumCO2=SumCO2,
SumCO2=SumCO2,
SumCO2=SumCO2,
SumCO2=SumCO2,
SumCO2=SumCO2,
pH=pH,
pH=pH,
pH=pH,
TA=TA,
TA=TA,
TA=TA)
CO2=CO2)
fCO2=fCO2)
CO2=CO2)
fCO2=fCO2)
################################################################
# Cloning the aquaenv system: 1 to 1 and with different pH or TA
################################################################
S
<- 30
t
<- 15
SumCO2 <- 0.0020
TA
<- 0.00214
ae <- aquaenv(S, t, SumCO2=SumCO2, TA=TA)
aeclone1 <- aquaenv(ae=ae)
pH <- 9
aeclone2 <- aquaenv(ae=ae, pH=pH)
TA <- 0.002
aeclone3 <- aquaenv(ae=ae, TA=TA)
ae$pH
aeclone1$pH
aeclone2$TA
aeclone3$pH
#########################################################################
# Vectors as input variables (only ONE input variable may be a vector)
# (with full output: including the Revelle factor and the DSA properties)
#########################################################################
SumCO2 <- 0.0020
pH
<- 8
S
<- 30
t
<- 1:15
p
<- gauge_p(10)
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, revelle=TRUE, dsa=TRUE)
plot(ae, xval=t, xlab="T/(deg C)", newdevice=FALSE)
S <- 1:30
t <- 15
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, revelle=TRUE, dsa=TRUE)
plot(ae, xval=S, xlab="S", newdevice=FALSE)
aquaenv
S <- 30
p <- gauge_p(seq(1,1000, 100))
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, revelle=TRUE, dsa=TRUE)
plot(ae, xval=p, xlab="gauge pressure/bar", newdevice=FALSE)
TA <- 0.0023
S <- 30
t <- 1:15
d <- gauge_p(10)
ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA, revelle=TRUE, dsa=TRUE)
plot(ae, xval=t, xlab="T/(deg C)", newdevice=FALSE)
S <- 1:30
t <- 15
ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA, revelle=TRUE, dsa=TRUE)
plot(ae, xval=S, xlab="S", newdevice=FALSE)
S <- 30
p <- gauge_p(seq(1,1000, 100))
ae <- aquaenv(S, t, p, SumCO2=SumCO2, TA=TA, revelle=TRUE, dsa=TRUE)
plot(ae, xval=p, xlab="gauge pressure/bar", newdevice=FALSE)
##################################################################
# Calculating SumCO2 by giving a constant pH&CO2, pH&fCO2, pH&TA,
# TA&CO2, or TA&fCO2
##################################################################
fCO2
<- 0.0006952296
CO2
<- 2.678137e-05
pH
<- 7.888573
TA
<- 0.0021
S
t
p
<- 30
<- 15
<- gauge_p(10)
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, CO2=CO2, dsa=TRUE, revelle=TRUE)
ae$SumCO2
ae$revelle
ae$dTAdH
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, fCO2=fCO2)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, TA=TA)
ae$SumCO2
ae <- aquaenv(S, t, p, SumCO2=NULL, TA=TA, CO2=CO2)
ae$SumCO2
7
8
AquaEnv_package
ae <- aquaenv(S, t, p, SumCO2=NULL, TA=TA, fCO2=fCO2)
ae$SumCO2
t <- 1:15
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, CO2=CO2)
plot(ae, xval=t, xlab="T/(deg C)", mfrow=c(9,10), newdevice=FALSE)
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, CO2=CO2, revelle=TRUE, dsa=TRUE)
plot(ae, xval=t, xlab="T/(deg C)", newdevice=FALSE)
S <- 1:30
t <- 15
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, fCO2=fCO2, revelle=TRUE, dsa=TRUE)
plot(ae, xval=S, xlab="S", newdevice=FALSE)
S <- 30
p <- gauge_p(seq(1,1000, 100))
ae <- aquaenv(S, t, p, SumCO2=NULL, pH=pH, TA=TA, revelle=TRUE, dsa=TRUE)
plot(ae, xval=p, xlab="gauge pressure/bar", newdevice=FALSE)
## End(Not run)
AquaEnv_package
AquaEnv - an integrated development toolbox for aquatic chemical
model generation
Description
AquaEnv is an integrated development toolbox for aquatic chemical model generation focused on
(ocean) acidification and CO2 air-water exchange.
It contains all elements necessary to model the pH, the related CO2 air-water exchange, as well as
aquatic acid-base chemistry in general for an arbitrary marine, estuarine or freshwater system. Also
chemical batches can be modelled.
Next to the routines necessary to calculate desired information, AquaEnv also contains a suite of
tools to visualize this information. Furthermore, AquaEnv can not only be used to build dynamic
models of aquatic systems, but it can also serve as a simple desktop tool for the experimental aquatic
chemist to generate and visualize all possible derived information from a set of measurements with
one single easy to use R function.
Additionally, the sensitivity of the system to variations in the input variables can be visualized.
Details
Package:
Type:
Version:
AquaEnv
Package
1.1
AquaEnv_package
9
Date:
License:
2016-05-18
GNU Public License 2 or above
Author(s)
Karline Soetaert (Maintainer), Andreas F. Hofmann, Mathilde Hagens
References
Hagens M. and J.J. Middelburg, 2016 Generalised expressions for the response of pH to changes in
ocean chemistry. Geochimica et Cosmochimica Acta, in press.
Hofmann A. F., K. Soetaert, J.J. Middelburg, F. J. R. Meysman, 2010 AquaEnv: An Aquatic AcidBase Modelling Environment in R. Aquatic Geochemistry 16: 507-546.
Examples
## Not run:
## show examples (see respective help pages for details)
example(aquaenv)
## open the directory with source code of demos
browseURL(paste(system.file(package="AquaEnv"), "/demo", sep=""))
## run demos
demo(basicfeatures )
## show package vignette with tutorial about how to use aquaenv
vignette("AquaEnv")
edit(vignette("AquaEnv"))
browseURL(paste(system.file(package="AquaEnv"), "/doc", sep=""))
## show index file of package vignettes and documentation files
browseURL(paste(system.file(package="AquaEnv"), "/doc/index.html", sep=""))
## show documentation about private functions in the packet
browseURL(paste(system.file(package="AquaEnv"), "/doc/AquaEnv-PrivateFunctions.pdf", sep=""))
## show documentation about physical-chemical constants and formulae used in the packet
browseURL(paste(system.file(package="AquaEnv"), "/doc/AquaEnv-ConstantsAndFormulae.pdf", sep=""))
## End(Not run)
10
BufferFactors
as.data.frame.aquaenv as.data.frame.aquaenv
Description
PUBLIC function: converts an object of class aquaenv to a standard R data frame
Usage
## S3 method for class 'aquaenv'
as.data.frame(x, ...)
Arguments
x
object of type aquaenv
...
further arguments are passed on
Value
data frame containing all elements of aquaenv
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
BufferFactors
BufferFactors
Description
PUBLIC function: calculates buffer factors describing the sensitivity of pH and concentrations of
acid-base species to a change in ocean chemistry
Usage
BufferFactors(ae = NULL, parameters = NA, species = c("SumCO2"),
k_w = NULL, k_co2 = NULL, k_hco3 = NULL,
k_boh3 = NULL, k_hso4 = NULL,
k_hf = NULL, k1k2 = "lueker",
khf = "dickson", khso4 = "dickson")
BufferFactors
11
Arguments
ae
an object of class ’aquaenv’. An error is produced in case an object is provided
that is not of class ’aquaenv’,
parameters
a vector containing one or more of the following variables: "DIC" (mol/kgsoln), "TotNH3" (mol/kg-soln), "TotP" (mol/kg-soln), "TotNO3" (mol/kg-soln),
"TotNO2" (mol/kg-soln), "TotS" (mol/kg-soln), "TotSi" (mol/kg-soln), "TB"
(mol/kg-soln), "TotF" (mol/kg-soln), "TotSO4" (mol/kg-soln), "sal" (-), "temp"
(deg C), "pres" (bar), "Alk" (mol/kg-soln). If a variable is not supplied and no
object of class ’aquaenv’ is provided, default values are assigned following Table 4 of Hagens and Middelburg (2016). If both ae and parameters are supplied,
given parameters will overwrite the corresponding values of ae
species
a vector containing one or more of the following variables: "SumCO2", "SumNH4",
"SumH3PO4", "SumHNO3", "SumHNO2", "SumH2S", "SumSiOH4", "SumBOH3", "SumHF", "SumH2SO4", "CO2", "HCO3", "CO3", "BOH3", "BOH4",
"OH", "H3PO4", "H2PO4", "HPO4", "PO4", "SiOH4", "SiOOH3", "SiO2OH2",
"H2S", "HS", "S2min", "NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F",
"HNO3", "NO3", "HNO2", "NO2". Default is c("SumCO2"). This vector defines the species for which the sensitivities are calculated
k_w
a fixed K\_W can be specified
k_co2
a fixed K\_CO2 can be specified
k_hco3
a fixed K\_HCO3 can be specified
k_boh3
a fixed K\_BOH3 can be specified
k_hso4
a fixed K\_HSO4 can be specified
k_hf
a fixed K\_HF can be specified
k1k2
either "lueker" (default, Lueker2000), "roy" (Roy1993a), or "millero" (Millero2006)
for K\_CO2 and K\_HCO3
khf
either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) for K\_HF
khso4
either "dickson" (default, Dickson1990) or "khoo" (Khoo1977) for K\_HSO4
Value
a list containing the objects "ae", "dTA.dH", "dtotX.dH", "dTA.dX", "dtotX.dX", "dTA.dpH", "dtotX.dpH",
"dH.dTA", "dH.dtotX", "dX.dTA", "dX.dtotX", "dpH.dTA", "dpH.dtotX", "beta.H" and "RF".
The object ’ae’ is of class ’aquaenv’ and refers to the output of the aquaenv function that is always
run as part of BufferFactors. Consult the vignette of AquaEnv for more information on this object.
The other objects are vectors with the length and names of the input species. Exceptions here are
dH.dtotX and dpH.dtotX, which also contain the numerically estimated sensitivities with respect
to salinity, pressure and temperature, as well as two factors related to pH scale conversion (see the
AquaEnv vignette for details on these latter conversion factors).
In case species are defined which corresponding total concentration equals zero, the corresponding
output produces ’NaN’. This is with the exception of "dTA.dH" and "dTA.dpH", which are always
calculated as they are linked to beta.H. Additionally, the Revelle factor is always calculated, as the
function ’aquaenv’ requires that the carbonate system be specified.
12
c.aquaenv
Author(s)
Mathilde Hagens (<[email protected]>)
References
Hagens M. and J.J. Middelburg, 2016 Generalised expressions for the response of pH to changes in
ocean chemistry. Geochimica et Cosmochimica Acta, in press.
Examples
## Not run:
# Default run
BufferFactors()
# All carbonate system species
BufferFactors(species = c("CO2", "HCO3", "CO3"))
# Total concentrations of all species
BufferFactors(species = c("SumCO2", "SumNH4", "SumH3PO4", "SumHNO3",
"SumHNO2", "SumH2S", "SumSiOH4", "SumBOH3",
"SumHF", "SumH2SO4"))
# Different carbonate system equilibrium constants
BufferFactors(k1k2 = "roy")
# Object of class 'aquaenv' as input
ae_input <- aquaenv(S=35, t=25, SumCO2 = 0.0020, pH = 8.1,
skeleton = TRUE)
BufferFactors(ae = ae_input)
# Produces some NaNs as certain total concentrations are zero
BufferFactors(ae = ae_input,
species = c("SumCO2", "SumNH4", "SumH3PO4", "SumHNO3",
"SumHNO2", "SumH2S", "SumSiOH4", "SumBOH3",
"SumHF", "SumH2SO4"))
# Object of class 'aquaenv' as input, but different total alkalinity
parameters <- c(Alk = 0.0022)
BufferFactors(ae = ae_input, parameters = parameters)
## End(Not run)
c.aquaenv
c.aquaenv
Description
PRIVATE function: adds an element to an object of class aquaenv
ConcRelCl
13
Usage
## S3 method for class 'aquaenv'
c(aquaenv, x, ...)
Arguments
aquaenv
object of class aquaenv
x
a vector of the form c(value, name) representing the element to be inserted into
the object of class aquaenv
...
further arguments will be passed
Value
object of class aquaenv with the added element
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
ConcRelCl
ConcRelCl
Description
PUBLIC data frame: a collection of concentrations of key chemical species in seawater, relative
with respect to chlorinity (DOE1994))
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
convert
convert
Description
PUBLIC function: converts either a single value (the pH scale of a pH value, the pH scale of a
dissociation constant (K*), the unit of a concentration value), or all elements of a special unit or pH
scale in an object of class aquaenv
14
convert
Arguments
x
vartype
what
S
t
p
SumH2SO4
SumHF
khf
khso4
from
to
factor
convattr
object to be converted: either a single value (pH value, K* value, or concentration value) or an object of class aquaenv
only valid if x is a single value: the type of x, either "pHscale", "KHscale", or
"conc"
only valid if x is a single value: only valid if x is a single value: the type of
conversion to be done, for pH scales one of "free2tot", "free2sws", "free2nbs",
... (any combination of "free", "tot", "sws", and "nbs"); for concentrations one of
"molar2molal", "molar2molin", ... (any combination of "molar" (mol/l), "molal"
(mol/kg-H2O), and "molin" (mol/kg-solution))
only valid if x is a single value: salinity (in practical salinity units: no unit)
only valid if x is a single value: temperature in degrees centigrade
only valid if x is a single value: gauge pressure (total pressure minus atmospheric pressure) in bars
only valid if x is a single value: total sulfate concentration in mol/kg-solution; if
not supplied this is calculated from S
only valid if x is a single value: total fluoride concentration in mol/kg-solution;
if not supplied this is calculated from S
only valid if x is a single value: either "dickson" (default, Dickson1979a) or
"perez" (Perez1987a) for K\_HF
only valid if x is a single value: either "dickson" (default, Dickson1990) or
"khoo" (Khoo1977) for K\_HSO4
only valid if x is an object of class aquaenv: the unit which needs to be converted
(as a string; must be a perfect match)
only valid if x is an object of class aquaenv: the unit to which the conversion
should go
only valid if x is an object of class aquaenv: the conversion factor to be applied:
can either be a number (e.g. 1000 to convert from mol to mmol), or any of the
conversion factors given in an object of class aquaenv
only valid if x is an object of class aquaenv: which attribute should be converted?
can either be "unit" or "pH scale"
Details
Possible usages are
convert(x, vartype, what, S, t, p, SumH2SO4, SumHF, khf)
convert(x, from, to, factor, convattr)
Value
converted single value or object of class aquaenv with converted elements
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
DeltaPcoeffs
15
Examples
## Not run:
### 1
#####
t <- 15
S <- 10
pH_NBS
<- 8.142777
SumCO2molar <- 0.002016803
pH_free
<- convert(pH_NBS,
"pHscale", "nbs2free",
S=S, t=t)
SumCO2molin <- convert(SumCO2molar, "conc",
"molar2molin", S=S, t=t)
ae <- aquaenv(S, t, SumCO2=SumCO2molin, pH=pH_free)
ae$pH
ae$SumCO2
### 2
#####
ae <- aquaenv(30,10)
ae$SumBOH3
ae <- convert(ae, "mol/kg-soln", "umol/kg-H2O", 1e6/ae$molal2molin, "unit")
ae$SumBOH3
## End(Not run)
DeltaPcoeffs
DeltaPcoeffs
Description
PUBLIC data frame: a collection of coefficients for the pressure correction of dissociation constants
and solubility products (Millero1995 WITH CORRECTIONS BY Lewis1998 (CO2Sys)!)
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
16
K0_CO2
gauge_p
gauge\_p
Description
PUBLIC function: calculates the gauge pressure (total pressure minus atmospheric pressure) from
the depth (in m) and the latitude (in degrees: -90 to 90) and the atmospheric pressure (in bar)
Usage
gauge_p(d, lat=0, Pa=1.01325)
Arguments
d
water depth in meters
lat
latitude in degrees: -90 to 90, standard: 0
Pa
atmospheric pressure in bar, standard: 1 atm (at sea level)
Value
gauge pressure (total pressure minus atmospheric pressure) p in bars
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Fofonoff1983
Examples
gauge_p(100)
plot(gauge_p(1:100))
K0_CO2
K0\_CO2
Description
PUBLIC function: calculates the Henry’s constant (solubility) for CO2
Usage
K0_CO2(S, t)
K0_O2
17
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
Value
the Henry’s constant for CO2 in mol/(kg-solution*atm)
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Weiss1974, DOE1994, Millero1995, Zeebe2001
Examples
K0_CO2(35, 15)
plot(K0_CO2(35, 1:25), xlab="temperature / degC")
K0_O2
K0\_O2
Description
PUBLIC function: calculates the Henry’s constant (solubility) for O2
Usage
K0_O2(S, t)
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
Value
the Henry’s constant for CO2 in mol/(kg-solution*atm)
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
derived from a formulation for [O2]sat given in Weiss1970
18
Ksp_aragonite
Examples
K0_O2(35, 15)
plot(K0_O2(35, 1:25), xlab="temperature / degC")
Ksp_aragonite
Ksp\_aragonite
Description
PUBLIC function: calculates the solubility product for aragonite
Usage
Ksp_aragonite(S, t, p=0)
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
Value
the solubility product for aragonite in (mol/kg-solution)2
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Mucci1983, Boudreau1996
Examples
Ksp_aragonite(35, 15)
Ksp_aragonite(35, 15, 10)
plot(Ksp_aragonite(35, 1:25), xlab="temperature / degC")
Ksp_calcite
Ksp_calcite
19
Ksp\_calcite
Description
PUBLIC function: calculates the solubility product for aragonite
Usage
Ksp_calcite(S, t, p=0)
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
Value
the solubility product for calcite in (mol/kg-solution)2
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Mucci1983, Boudreau1996
Examples
Ksp_calcite(35, 15)
Ksp_calcite(35, 15, 10)
plot(Ksp_aragonite(35, 1:25), xlab="temperature / degC")
K_BOH3
K\_BOH3
Description
PUBLIC function: calculates the dissociation constant of B(OH)3
Usage
K_BOH3(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
20
K_CO2
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of B(OH)3 in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Dickson1990, DOE1994, Millero1995 (molality version given), Zeebe2001
Examples
K_BOH3(35, 15)
K_BOH3(35, 15, 10)
K_BOH3(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_BOH3(35, 1:25), xlab="temperature / degC")
K_CO2
K\_CO2
Description
PUBLIC function: calculates the dissociation constant of CO2
Usage
K_CO2(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, k1k2="lueker", khf="dickson", khso4="dickson")
K_H2PO4
21
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
k1k2
"lueker", "roy", or "millero": specifies the S, t, dependency to be used. Default
is "lueker". (see section below for references)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of CO2 in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
k1k2 = "roy": Roy1993b, DOE1994, Millero1995, Zeebe2001; k1k2 = "lueker": Lueker2000; k1k2
= "millero": Millero2006
Examples
K_CO2(35, 15)
K_CO2(35, 15, 10)
K_CO2(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_CO2(35, 1:25), xlab="temperature / degC")
K_H2PO4
K\_H2PO4
Description
PUBLIC function: calculates the dissociation constant of H2PO4
Usage
K_H2PO4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
22
K_H2S
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of H2PO4 in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Millero1995 (original, SWS pH version), DOE1994 (in a later revision cites Millero1995)
Examples
K_H2PO4(35, 15)
K_H2PO4(35, 15, 10)
K_H2PO4(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_H2PO4(35, 1:25), xlab="temperature / degC")
K_H2S
K\_H2S
Description
PUBLIC function: calculates the dissociation constant of H2S
Usage
K_H2S(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
K_H3PO4
23
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of H2S in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Millero1988, Millero1995
Examples
K_H2S(35, 15)
K_H2S(35, 15, 10)
K_H2S(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_H2S(35, 1:25), xlab="temperature / degC")
K_H3PO4
K\_H3PO4
Description
PUBLIC function: calculates the dissociation constant of H3PO4
Usage
K_H3PO4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
24
K_HCO3
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of H3PO4 in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Millero1995 (original, SWS pH version), DOE1994 (in a later revision cites Millero1995)
Examples
K_H3PO4(35, 15)
K_H3PO4(35, 15, 10)
K_H3PO4(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_H3PO4(35, 1:25), xlab="temperature / degC")
K_HCO3
K\_HCO3
Description
PUBLIC function: calculates the dissociation constant of HCO3
Usage
K_HCO3(S, t, p=0, SumH2SO4=NULL, SumHF=NULL,
k1k2="lueker", khf="dickson", khso4="dickson")
K_HF
25
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
k1k2
"lueker", "roy", or "millero": specifies the S, t, dependency to be used. Default
is "lueker". (see section below for references)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of HCO3 in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
k1k2 = "roy": Roy1993b, DOE1994, Millero1995, Zeebe2001; k1k2 = "lueker": Lueker2000; k1k2
= "millero": Millero2006
Examples
K_HCO3(35, 15)
K_HCO3(35, 15, 10)
K_HCO3(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_HCO3(35, 1:25), xlab="temperature / degC")
K_HF
K\_HF
Description
PUBLIC function: calculates the dissociation constant of HF
Usage
K_HF(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
26
K_HPO4
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
khf
"dickson" or "perez": specifies the S, t, dependency to be used. Default is "dickson". (see section below for references)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of HF in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
khf = "dickson": Dickson1979a, Dickson1987, Roy1993b, DOE1994, Millero1995, Zeebe2001;
khf = "perez": Perez1987
Examples
K_HF(35, 15)
K_HF(35, 15, 10)
plot(K_HF(35, 1:25), xlab="temperature / degC")
K_HPO4
K\_HPO4
Description
PUBLIC function: calculates the dissociation constant of HPO4
Usage
K_HPO4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
K_HSO4
27
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of HPO4 in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Millero1995 (original, SWS pH version), DOE1994 (in a later revision cites Millero1995)
Examples
K_HPO4(35, 15)
K_HPO4(35, 15, 10)
K_HPO4(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_HPO4(35, 1:25), xlab="temperature / degC")
K_HSO4
K\_HSO4
Description
PUBLIC function: calculates the dissociation constant of HSO4
Usage
K_HSO4(S, t, p=0, khso4="dickson")
28
K_NH4
Arguments
S
t
p
khso4
salinity in practical salinity units (i.e. no unit)
temperature in degrees centigrade
gauge pressure (total pressure minus atmospheric pressure) in bars
"dickson" or "khoo": specifies the S, t, dependency to be used. Default is "dickson". (see section below for references)
Value
the dissociation constant of HSO4 in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
"dickson": Dickson1990, DOE1994, Zeebe2001; "khoo": Khoo1977, Roy1993, Millero1995
Examples
K_HSO4(35, 15)
K_HSO4(35, 15, 10)
plot(K_HSO4(35, 1:25), xlab="temperature / degC")
K_NH4
K\_NH4
Description
PUBLIC function: calculates the dissociation constant of NH4
Usage
K_NH4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
Arguments
S
t
p
SumH2SO4
SumHF
khf
khso4
salinity in practical salinity units (i.e. no unit)
temperature in degrees centigrade
gauge pressure (total pressure minus atmospheric pressure) in bars
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
K_SiOH4
29
Value
the dissociation constant of NH4 in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Millero1995a, Millero1995, corrected by Lewis1998
Examples
K_NH4(35, 15)
K_NH4(35, 15, 10)
K_NH4(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_NH4(35, 1:25), xlab="temperature / degC")
K_SiOH4
K\_SiOH4
Description
PUBLIC function: calculates the dissociation constant of SiOH4
Usage
K_SiOH4(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of SiOH4 in mol/kg-solution on the free proton pH scale
30
K_SiOOH3
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Millero1988, DOE1994, Millero1995
Examples
K_SiOH4(35, 15)
K_SiOH4(35, 15, 10)
K_SiOH4(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_SiOH4(35, 1:25), xlab="temperature / degC")
K_SiOOH3
K\_SiOOH3
Description
PUBLIC function: calculates the dissociation constant of SiOOH3
Usage
K_SiOOH3(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the dissociation constant of SiOOH3 in mol/kg-solution on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
K_W
31
References
Wischmeyer2003 (incl. corrections)
Examples
K_SiOOH3(35, 15)
K_SiOOH3(35, 15, 10)
K_SiOOH3(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_SiOOH3(35, 1:25), xlab="temperature / degC")
K_W
K\_W
Description
PUBLIC function: calculates the ion product of H2O
Usage
K_W(S, t, p=0, SumH2SO4=NULL, SumHF=NULL, khf="dickson", khso4="dickson")
Arguments
S
salinity in practical salinity units (i.e. no unit)
t
temperature in degrees centigrade
p
gauge pressure (total pressure minus atmospheric pressure) in bars
SumH2SO4
total sulfate concentration in mol/kg-solution (calculated from S if not supplied)
SumHF
total fluoride concentration in mol/kg-solution (calculated from S if not supplied)
khf
S, t relation for K\_HF needed for scale conversion: either "dickson" (default,
Dickson1979a) or "perez" (Perez1987a)
khso4
S, t relation for K\_HSO4 needed for scale conversion: either "dickson" (default,
Dickson1990) or "khoo" (Khoo1977)
Value
the ion product of H2O in (mol/kg-solution)2 on the free proton pH scale
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Millero1995 (SWS pH version), DOE1994 (cites Millero1995), Zeebe2001
32
MeanMolecularMass
Examples
K_W(35, 15)
K_W(35, 15, 10)
K_W(S=35, t=15, p=10, SumH2SO4=0.03)
plot(K_W(35, 1:25), xlab="temperature / degC")
length.aquaenv
length.aquaenv
Description
PRIVATE function: returns the (maximal) length of the elements in an object of class aquaenv (i.e.
> 1 if one of the input variables was a vector)
Usage
## S3 method for class 'aquaenv'
length(x, ...)
Arguments
x
object of class aquaenv
...
further arguments will be passed
Value
the maximal length of the elements in the object of class aquaenv
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
MeanMolecularMass
MeanMolecularMass
Description
PUBLIC data frame: a collection of mean molecular masses of key chemical species in seawater in
g/mol (DOE1994))
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
merge.aquaenv
merge.aquaenv
33
merge.aquaenv
Description
PRIVATE function: merges the elements of two objects of class aquaenv: element names are taken
from the first argument, the elements of which are also first in the merged object
Usage
## S3 method for class 'aquaenv'
merge(x, y, ...)
Arguments
x
object of class aquaenv: this is where the element names are taken from
y
object of class aquaenv: must contain at leas all the element (names) as aquaenv1,
extra elements are ignored
...
further arguments will be passed
Value
object of class aquaenv with merged elements
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
PhysChemConst
PhysChemConst
Description
PUBLIC list: a collection of physical and chemical constants
Value
A list containing:
R
(bar*cm3)/(mol*K) the gas constant (corrected after Lewis1998, in Millero1995:
R = 83.131); digits extended after Dickson2007)
F
C/mol the Faraday constant (charge per mol of electrons) (N\_A*e-): Dickson2007
uMolToMol
conversion factor from umol to mol
absZero
absolute zero in degrees centigrade
34
plot.aquaenv
e
relative dielectric constanf of seawater (Zeebe2001)
K_HNO2
dissociation constant of HNO2: mol/l, NBS pH scale, hybrid constant (Riordan2005)
K_HNO3
dissociation constant of HNO3: assumed on mol/kg-soln and free pH scale,
stoichiometric constant (Soetaert pers. comm.)
K_H2SO4
dissociation constant of H2SO4: assumed on mol/kg-soln and free pH scale,
stoichiometric constant (Atkins1996)
K_HS
dissociation constant of HHS: assumed on mol/kg-soln and free pH scale, stoichiometric constant (Atkins1996)
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
plot.aquaenv
plot.aquaenv
Description
PUBLIC function: high level plot function for objects of class aquaenv
Arguments
x
object of class aquaenv
xval
only valid if bjerrum=FALSE: a vector of the (maximal) length of the elements
of aquaenv against which they are to be plotted
what
a list of names of the elements of aquaenv that are to be plotted, if not supplied
and bjerrum=FALSE and cumulative=FALSE: all elements are plotted, if not
supplied and bjerrum=TRUE then what is set to be c("CO2", "HCO3", "CO3",
"BOH3", "BOH4", "OH", "H3PO4", "H2PO4", "HPO4", "PO4", "SiOH4", "SiOOH3",
"SiO2OH2", "H2S", "HS", "S2min", "NH4", "NH3", "H2SO4", "HSO4", "SO4",
"HF", "F", "HNO3", "NO3", "HNO2", "NO2"), needs to be supplied for cumulative=TRUE
bjerrum
flag: TRUE = a bjerrum plot is done (by calling bjerrumplot)
cumulative
flag: TRUE = a cumulative plot is done (by calling cumulativeplot)
newdevice
flag: if TRUE, new plot device is opened
setpar
flag: if TRUE parameters are set with the function par
xlab
x axis label
log
only valif if bjerrum=TRUE: should the plot be on a logarithmic y axis?
total
only valid if cumulative=TRUE: should the sum of all elements specified in what
be plotted as well?
device
the device to plot on; default: "x11" (can also be "eps" or "pdf")
filename
filename to be used if "eps" or "pdf" is selected for device
plot.aquaenv
35
size
the size of the plot device; default: 12 (width) by 10 (height) inches
ylim
standard plot parameter; if not supplied it will be calculated by range() of the
elements to plot
lwd
standard plot parameter; width of the lines in the plot
mgp
standard plot parameter; default: axis title on line 1.8, axis labels on line 0.5,
axis on line 0
mar
standard plot parameter; default: margin of 3 lines bottom and left and 0.5 lines
top and right
oma
standard plot parameter; default: no outer margin
palette
only valid if bjerrum=TRUE or cumulative=TRUE: a vector of colors to use in
the plot (either numbers or names given in colors())
legendposition
only valid if bjerrum=TRUE or cumulative=TRUE: position of the legend
legendinset
only valid if bjerrum=TRUE or cumulative=TRUE: standard legend parameter
inset
legendlwd
only valid if bjerrum=TRUE or cumulative=TRUE: standard legend parameter
lwd: line width of lines in legend
bg
only valid if bjerrum=TRUE or cumulative=TRUE: standard legend parameter:
default background color: white
y.intersp
standard legend parameter; if cumulative=TRUE then default: 1.2 lines space
between the lines in the legend
...
further arguments are passed on to the plot function
Details
Top level generic usage is
plot.aquaenv(x, xval, what=NULL, bjerrum=FALSE,
cumulative=FALSE, newdevice=TRUE, setpar=TRUE,
device="x11", ...)
Generic usages for standard plotting are
plot.aquaenv(x, xval, ...)
plot.aquaenv(x, xval, what, mfrow=c(1,1), size=c(7,7), ...)
Generic usage for creating a bjerrum plot is
plot.aquaenv(x, what, log=FALSE, palette=NULL,
device="x11", filename="aquaenv",
size=c(12,10), ylim=NULL, lwd=2, xlab="free scale pH",
mgp=c(1.8, 0.5, 0), mar=c(3,3,0.5,0.5), oma=c(0,0,0,0),
legendposition="bottomleft", legendinset=0.05,
legendlwd=4, bg="white", newdevice=TRUE, setpar=TRUE,
device="x11",...)
36
plot.aquaenv
Generic usage for creating a cumulative plot is
plot.aquaenv(x, xval, what, total=TRUE, palette=NULL,
device="x11", filename="aquaenv", size=c(12,10), ylim=NULL,
lwd=2, mgp=c(1.8, 0.5, 0), mar=c(3,3,0.5,0.5), oma=c(0,0,0,0),
legendposition="bottomleft", legendinset=0.05, legendlwd=4,
bg="white", y.intersp=1.2, newdevice=TRUE, setpar=TRUE,
device="x11",...)
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Examples
## Not run:
### 0
#####
A <- aquaenv(35, 15, SumCO2=0.003, TA=seq(0.001,0.004, 0.0001))
plot(A, xval=A$TA, xlab="[TA]/(mol/kg-soln)")
plot(A, what=c("CO2", "HCO3", "CO3"), bjerrum=TRUE, log=TRUE)
plot(A, xval=A$TA, xlab="[TA]/(mol/kg-soln)", what=c("CO2", "HCO3", "CO3"),
cumulative=TRUE, ylab="mol/kg-soln", ylim=c(0,0.0031))
### 1
#####
SumCO2 <- 0.0020
pH
<- 8
S
<- 30
t
<- 1:15
p
<- 10
ae <- aquaenv(S, t, p, SumCO2=SumCO2, pH=pH, revelle=TRUE, dsa=TRUE)
plot(ae, xval=t, xlab="T/(deg C)", newdevice=FALSE)
### 2
#####
S <- 35
t <- 15
SumCO2 <- 0.003500
SumNH4 <- 0.000020
mass_sample <- 0.01 # the mass of the sample solution in kg
mass_titrant <- 0.02 # the total mass of the added titrant solution in
# kg
conc_titrant <- 0.01 # the concentration of the titrant solution in
# mol/kg-soln
plot.aquaenv
S_titrant
steps
type
37
<- 0.5
#
#
#
<- 50
#
#
<- "HCl"
the salinity of the titrant solution (the
salinity of a solution with a ionic strength of
0.01 according to: I = (19.924 S) / (1000 - 1.005S)
the amount of steps the mass of titrant is added
in
pHstart <- 11.3
ae <- titration(aquaenv(S=S, t=t, SumCO2=SumCO2, SumNH4=SumNH4,
pH=pHstart), mass_sample, mass_titrant, conc_titrant,
S_titrant, steps, type)
# plotting everything
plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]",
mfrow=c(10,10))
# plotting selectively
size <- c(12,8) #inches
mfrow <- c(4,4)
what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
"NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "pCO2")
plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]",
what=what, size=size, mfrow=mfrow)
plot(ae, xval=ae$pH, xlab="free scale pH", what=what, size=size,
mfrow=mfrow)
# different x values
plot(ae, xval=ae$delta_conc_titrant, xlab="[HCl] offset added
[mol/kg-soln]", what=what, size=size, mfrow=mfrow)
plot(ae, xval=ae$delta_moles_titrant, xlab="HCl added [mol]", what=what,
size=size, mfrow=mfrow, newdevice=FALSE)
# bjerrum plots
plot(ae, bjerrum=TRUE)
what <- c("CO2", "HCO3", "CO3")
plot(ae, what=what, bjerrum=TRUE)
plot(ae, what=what, bjerrum=TRUE, lwd=4, palette=c("cyan", "magenta",
"yellow"), bg="gray", legendinset=0.1, legendposition="topleft")
what
<- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3",
38
plot.aquaenv
"H2SO4", "HSO4", "SO4", "HF", "F")
plot(ae, what=what, bjerrum=TRUE, log=TRUE, newdevice=FALSE)
plot(ae, what=what, bjerrum=TRUE, log=TRUE, ylim=c(-6,-1),
legendinset=0, lwd=3, palette=c(1,3,4,5,6,colors()[seq(100,250,6)]))
### 3
#####
parameters <- list(
t
= 15
S
= 35
SumCO2_t0
TA_t0
= 0.002
= 0.0022
kc
= 0.5
, # degrees C
, # psu
, # mol/kg-soln
, # mol/kg-soln
(comparable to Wang2005)
(comparable to Millero1998)
, # 1/d
proportionality factor
#
for air-water exchange
= 0.000001 , # mol/(kg-soln*d) max rate of calcium
#
carbonate precipitation
= 2.0
, # exponent for kinetic
#
rate law of precipitation
kp
n
modeltime
= 20
outputsteps = 100
)
, # d
#
duration of the model
number of outputsteps
boxmodel <- function(timestep, currentstate, parameters)
{
with (
as.list(c(currentstate,parameters)),
{
ae
<- aquaenv(S=S, t=t, SumCO2=SumCO2, pH=-log10(H), SumSiOH4=0,
SumBOH3=0, SumH2SO4=0, SumHF=0, dsa=TRUE)
Rc
Rp
<- kc * ((ae$CO2_sat) - (ae$CO2))
<- kp * (1-ae$omega_calcite)^n
dSumCO2 <- Rc - Rp
dHRc
dHRp
dH
<- (
-(ae$dTAdSumCO2*Rc
))/ae$dTAdH
<- (-2*Rp -(ae$dTAdSumCO2*(-Rp)))/ae$dTAdH
<- dHRc + dHRp
ratesofchanges <- c(dSumCO2, dH)
processrates
outputvars
}
}
)
<- c(Rc=Rc, Rp=Rp)
<- c(dHRc=dHRc, dHRp=dHRp)
return(list(ratesofchanges, list(processrates, outputvars, ae)))
sample_dickson1981
39
with (as.list(parameters),
{
aetmp <- aquaenv(S=S, t=t, SumCO2=SumCO2_t0,
TA=TA_t0, SumSiOH4=0, SumBOH3=0,
SumH2SO4=0, SumHF=0)
H_t0 <- 10^(-aetmp$pH)
initialstate <<- c(SumCO2=SumCO2_t0, H=H_t0)
times
<<- seq(0,modeltime,(modeltime/outputsteps))
output
<<- as.data.frame(vode(initialstate,times,
boxmodel,parameters, hmax=1))
})
what
<- c("SumCO2", "TA", "Rc", "Rp",
"omega_calcite", "pH", "dHRc", "dHRp")
plot(aquaenv(ae=output, from.data.frame=TRUE), xval=output$time,
xlab="time/d", mfrow=c(3,3), size=c(15,10), what=what)
what <- c("dHRc", "dHRp")
plot(aquaenv(ae=output, from.data.frame=TRUE), xval=output$time,
xlab="time/d", what=what, ylab="mol-H/(kg-soln*d)",
legendposition="topright", cumulative=TRUE)
## End(Not run)
sample_dickson1981
sample\_dickson1981
Description
PUBLIC dataset: theoretical titration curve for TA determination as given in table 1 of Dickson1981
Meta-data:
x-value
y-value
t
S
mass\_sample
conc\_titrant
TA
SumCO2
SumBOH3
SumH2SO4
mass of titrant added (in g)
pH measured on the free proton scale
25
35
200
0.3000
0.00245
0.00220
0.00042
0.02824
degC
g
mol/kg-soln
mol/kg-soln
mol/kg-soln
mol/kg-soln
mol/kg-soln
40
TAfit
0.00007
4.32e-14
1.00e-6
8.20e-10
1.78e-9
1/1.23e1
1/4.08e2
SumHF
K\_W
K\_CO2
K\_HCO3
K\_BOH3
K\_HSO4
K\_HF
mol/kg-soln
(mol/kg-soln)*(mol/kg-soln)
mol/kg-soln
mol/kg-soln
mol/kg-soln
mol/kg-soln
mol/kg-soln
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
sample_dickson2007
sample\_dickson2007
Description
PUBLIC dataset: titration curve for TA determination as given on p. 11 of SOP3b in Dickson2007
Metadata:
x-value
y-value
mass of titrant added (in cubic centimeters)
E in V
t
S
mass\_sample
conc\_titrant
density titrant
calculated TA
calculated E0
24.25
33.923
140.32
0.10046
1.02393
2260.06
0.394401
degC
g
mol/kg-soln
g/cm3
umol/kg-soln
V
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
TAfit
TAfit
TAfit
41
Description
PUBLIC function: calculates [TA] and [SumCO2] (and optionally K\_C02 and E0) from a titration
curve using an optimization procedure (nls.lm from R package minpack.lm)
Usage
TAfit(ae, titcurve, conc_titrant, mass_sample, S_titrant=NULL,
TASumCO2guess=0.0025, E0guess=0.4, type="HCl", Evals=FALSE,
electrode_polarity="pos", K_CO2fit=FALSE,
equalspaced=TRUE, seawater_titrant=FALSE,
pHscale="free", debug=FALSE, k_w=NULL, k_co2=NULL, k_hco3=NULL,
k_boh3=NULL, k_hso4=NULL, k_hf=NULL,
nlscontrol=nls.lm.control(), verbose=FALSE,
k1k2="roy", khf="dickson", datxbegin=0, SumCO2Zero=FALSE)
Arguments
ae
an object of type aquaenv: minimal definition, contains all information about
the system: T, S, d, total concentrations of nutrients etc (Note that it is possible
to give values for SumBOH4, SumHSO4, and SumHF in the sample other than
the ones calculated from salinity)
titcurve
a table containing the titration curve: basically a series of tuples of added titrant
solution mass and pH values (pH on free proton scale) or E values in V
conc_titrant
concentration of the titrant solution in mol/kg-soln
mass_sample
the mass of the sample solution in kg
S_titrant
the salinity of the titrant solution, if not supplied it is assumed that the titrant
solution has the same salinity as the sample solution
TASumCO2guess
a first guess for [TA] and [SumCO2] to be used as initial values for the optimization procedure
E0guess
first guess for E0 in V
type
the type of titrant: either "HCl" or "NaOH"
Evals
are the supplied datapoints pH or E (V) values?
electrode_polarity
either "pos" or "neg": how is the polarity of the Electrode: E = E0 -(RT/F)ln(H+)
("pos") or -E = E0 -(RT/F)ln(H+) ("neg")?
K_CO2fit
should K\_CO2 be fitted as well?
equalspaced
are the mass values of titcurve equally spaced?
seawater_titrant
is the titrant based on natural seawater? (does it contain SumBOH4, SumHSO4,
and SumHF in the same proportions as seawater, i.e., correlated to S?); Note that
you can only assume a seawater based titrant (i.e. SumBOH4, SumHSO4, and
SumHF ~ S) or a water based titrant (i.e. SumBOH4, SumHSO4, and SumHF
= 0). It is not possible to give values for SumBOH4, SumHSO4, and SumHF of
the titrant.
42
TAfit
pHscale
either "free", "total", "sws" or "nbs": if the titration curve contains pH data: on
which scale is it measured?
debug
debug mode: the last simulated titration tit, the converted pH profile calc, and
the nls.lm output out are made global variables for investigation and plotting
k_w
a fixed K\_W can be specified
k_co2
a fixed K\_CO2 can be specified; used for TA fitting: give a K\_CO2 and NOT
calculate it from T and S: i.e. K\_CO2 can be fitted in the routine as well
k_hco3
a fixed K\_HCO3 can be specified
k_boh3
a fixed K\_BOH3 can be specified
k_hso4
a fixed K\_HSO4 can be specified
k_hf
a fixed K\_HF can be specified
nlscontrol
nls.lm.control() can be specified
verbose
verbose mode: show the traject of the fitting in a plot
k1k2
either "roy" (default, Roy1993a) or "lueker" (Lueker2000) for K\_CO2 and
K\_HCO3.
khf
either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) for K\_HF
datxbegin
at what x value (amount of titrant added) does the supplied curve start? (i.e. is
the complete curve supplied or just a part?)
SumCO2Zero
should SumCO2==0?
Value
a list of up to five values ([TA] in mol/kg-solution, [SumCO2] in mol/kg-solution, E0 in V, K1 in
mol/kg-solution and on free scale, sum of the squared residuals)
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Examples
## Not run:
####################################
# Calculating TA from titration data
####################################
#### 1.) proof of concept ##########
####################################
####################################
# generate "data":
S <- 35
t <- 15
SumCO2
<- 0.002000
TAfit
43
TA
<- 0.002200
initial_ae <- aquaenv(S=S, t=t, SumCO2=SumCO2, TA=TA)
mass_sample <- 0.01 # the mass of the sample solution in kg
mass_titrant <- 0.003 # the total mass of the added titrant solution
# in kg
conc_titrant <- 0.01 # the concentration of the titrant solution in
# mol/kg-soln
S_titrant
<- 0.5
# the salinity of the titrant solution (the
# salinity of a solution with a ionic strength
# of 0.01 according to:
# I = (19.924 S) / (1000 - 1.005 S)
steps
<- 20
# the amount of steps the mass of titrant is
# added in
type
<- "HCl"
ae <- titration(initial_ae, mass_sample, mass_titrant, conc_titrant,
S_titrant, steps, type)
plot(ae, ae$delta_mass_titrant, what="pH", newdevice=FALSE)
# the input data for the TA fitting routine: a table with the added
# mass of the titrant and the resulting free scale pH
titcurve <- cbind(ae$delta_mass_titrant, ae$pH)
#
#
#
#
for the TA fitting procedure all total quantities except SumCO2
(SumNH4, SumH2S, SumH3PO4, SumSiOH4, SumHNO3, SumHNO2, SumBOH3,
SumH2SO4, SumHF) need to be known. However, the latter three
can be calculated from salinity as it is done in this example.
fit1 <- TAfit(initial_ae, titcurve, conc_titrant, mass_sample,
S_titrant)
fit1
# E (V) values as input variables: generate E values using
# E0=0.4 V and the nernst equation
tottitcurve <- convert(titcurve[,2], "pHscale", "free2sws", S=S,
t=t)
# (Nernst equation relates E to TOTAL [H+] (DOE1994, p.7,
# ch.4, sop.3), BUT, if fluoride is present, its SWS, so
# we use SWS!
Etitcurve
<- cbind(titcurve[,1], (0.4 - ((PhysChemConst$R/10)
*initial_ae$T/PhysChemConst$F)
*log(10^-tottitcurve))) # Nernst equation
fit2 <- TAfit(initial_ae, Etitcurve, conc_titrant, mass_sample,
S_titrant, Evals=TRUE, verbose=TRUE)
fit2
# k_co2 fitting: one K_CO2 (k_co2) for the whole titration curve
# is fitted, i.e. there is NO correction for K_CO2 changes due to
44
TAfit
# changing S due to mixing with the titrant
fit3 <- TAfit(initial_ae, titcurve, conc_titrant, mass_sample,
S_titrant, K_CO2fit=TRUE)
fit3
# assume the titrant has the same salinity as the sample
# (and is made up of natural seawater, i.e. containing SumBOH4,
# SumH2SO4 and SumHF as functions of S), then the "right" K_CO2
# should be fitted i.e we do NOT give the argument S_titrant
# and set the flag seawater_titrant to TRUE
ae
<- titration(initial_ae, mass_sample, mass_titrant,
conc_titrant, steps=steps, type=type,
seawater_titrant=TRUE)
titcurve <- cbind(ae$delta_mass_titrant, ae$pH)
fit4 <- TAfit(initial_ae, titcurve, conc_titrant, mass_sample,
K_CO2fit=TRUE, seawater_titrant=TRUE)
fit4
# fitting of TA, SumCO2, K_CO2 and E0
Etitcurve <- cbind(titcurve[,1], (0.4 - ((PhysChemConst$R/10)
*initial_ae$T/PhysChemConst$F)
*log(10^-titcurve[,2])))
fit5 <- TAfit(initial_ae, Etitcurve, conc_titrant, mass_sample,
K_CO2fit=TRUE, seawater_titrant=TRUE, Evals=TRUE)
fit5
# fitting of non equally spaced data:
neqsptitcurve <- rbind(titcurve[1:9,], titcurve[11:20,])
fit6 <- TAfit(initial_ae, neqsptitcurve, conc_titrant,
mass_sample, seawater_titrant=TRUE,
equalspaced=FALSE)
fit6
#add some "noise" on the generated data
noisetitcurve <- titcurve * rnorm(length(titcurve),
mean=1, sd=0.01) #one percent error possible
plot(ae, ae$delta_mass_titrant, what="pH", type="l", col="red",
xlim=c(0,0.003), ylim=c(3,8.1), newdevice=FALSE)
par(new=TRUE)
plot(noisetitcurve[,1],noisetitcurve[,2], type="l",
xlim=c(0,0.003), ylim=c(3,8.1))
fit7 <- TAfit(initial_ae, noisetitcurve, conc_titrant,
mass_sample, seawater_titrant=TRUE)
fit7
# 2.) test with generated data from Dickson1981 #
#################################################
#################################################
TAfit
conc_titrant = 0.3
# mol/kg-soln
mass_sample = 0.2
# kg
S_titrant
= 14.835 # is aequivalent to the ionic strength
# of 0.3 mol/kg-soln
SumBOH3 = 0.00042 # mol/kg-soln
SumH2SO4 = 0.02824 # mol/kg-soln
SumHF
= 0.00007 # mol/kg-soln
# convert mass of titrant from g to kg
sam <- cbind(sample_dickson1981[,1]/1000, sample_dickson1981[,2])
dicksonfit <- TAfit(aquaenv(t=25, S=35, SumBOH3=SumBOH3,
SumH2SO4=SumH2SO4, SumHF=SumHF), sam,
conc_titrant, mass_sample,
S_titrant=S_titrant, debug=TRUE)
dicksonfit
#TA
Dickson1981: 0.00245
#SumCO2 Dickson1981: 0.00220
# => not exactly the same! why?
# a.) does salinity correction (S_titrant) matter or not?
##########################################################
# without salinity correction
dicksontitration1 <- titration(aquaenv(t=25, S=35, SumCO2=0.00220,
SumBOH3=SumBOH3, SumH2SO4=SumH2SO4,
SumHF=SumHF, TA=0.00245),
mass_sample=mass_sample,
mass_titrant=0.0025,
conc_titrant=conc_titrant,
steps=50, type="HCl")
# with salinity correction
dicksontitration2 <- titration(aquaenv(t=25, S=35, SumCO2=0.00220,
SumBOH3=SumBOH3, SumH2SO4=SumH2SO4,
SumHF=SumHF, TA=0.00245),
mass_sample=mass_sample,
mass_titrant=0.0025,
conc_titrant=conc_titrant,
S_titrant=S_titrant,
steps=50, type="HCl")
plot(dicksontitration1, xval=dicksontitration1$delta_mass_titrant,
what="pH", xlim=c(0,0.0025), ylim=c(3,8.2), newdevice=FALSE,
col="red")
par(new=TRUE)
plot(dicksontitration2, xval=dicksontitration2$delta_mass_titrant,
what="pH", xlim=c(0,0.0025), ylim=c(3,8.2), newdevice=FALSE,
45
46
TAfit
col="blue")
par(new=TRUE)
plot(sam[,1], sam[,2], type="l", xlim=c(0,0.0025), ylim=c(3,8.2))
# => salinity correction makes NO difference, because the relation
# between total sample and added titrant is very large:
# salinity only drops from 35 to 34.75105
#BUT: there is an offset between the "Dickson" curve and our curve:
plot(dicksontitration2$pH - sam[,2])
# b.) does it get better if we fit K_CO2 as well?
#################################################
dicksonfit2 <- TAfit(aquaenv(t=25, S=35, SumBOH3=SumBOH3,
SumH2SO4=SumH2SO4, SumHF=SumHF), sam,
conc_titrant, mass_sample,
S_titrant=S_titrant, debug=TRUE,
K_CO2fit=TRUE)
dicksonfit2
#TA
Dickson1981: 0.00245
#SumCO2 Dickson1981: 0.00220
# => yes it does, but it is not perfect yet!
# c.) differing K values
#########################
# Dickson uses fixed K values that are slightly different than ours
dicksontitration3 <- titration(aquaenv(t=25, S=35, SumCO2=0.00220,
SumBOH3=SumBOH3, SumH2SO4=SumH2SO4,
SumHF=SumHF, TA=0.00245, k_w=4.32e-14,
k_co2=1e-6, k_hco3=8.20e-10,
k_boh3=1.78e-9, k_hso4=(1/1.23e1),
k_hf=(1/4.08e2)),
mass_sample=mass_sample,
mass_titrant=0.0025,
conc_titrant=conc_titrant,
steps=50, type="HCl",
S_titrant=S_titrant, k_w=4.32e-14,
k_co2=1e-6, k_hco3=8.20e-10,
k_boh3=1.78e-9, k_hso4=(1/1.23e1),
k_hf=(1/4.08e2))
plot(dicksontitration3, xval=dicksontitration3$delta_mass_titrant,
what="pH", xlim=c(0,0.0025), ylim=c(3,8.2), newdevice=FALSE,
col="blue")
par(new=TRUE)
plot(sam[,1], sam[,2], type="l", xlim=c(0,0.0025), ylim=c(3,8.2))
plot(dicksontitration3$pH - sam[,2])
# => no offset between the pH curves
# => exactly the same curves!
Technicals
47
dicksonfit3 <- TAfit(aquaenv(t=25, S=35, SumBOH3=SumBOH3,
SumH2SO4=SumH2SO4, SumHF=SumHF, k_w=4.32e-14,
k_co2=1e-6, k_hco3=8.20e-10, k_boh3=1.78e-9,
k_hso4=(1/1.23e1), k_hf=(1/4.08e2)),
sam, conc_titrant, mass_sample,
S_titrant=S_titrant, debug=TRUE,
k_w=4.32e-14, k_co2=1e-6, k_hco3=8.20e-10,
k_boh3=1.78e-9, k_hso4=(1/1.23e1),
k_hf=(1/4.08e2))
dicksonfit3
# PERFECT fit!
plot(sam[,1], sam[,2], xlim=c(0,0.0025), ylim=c(3,8.2), type="l")
par(new=TRUE)
plot(tit$delta_mass_titrant, calc, xlim=c(0,0.0025), ylim=c(3,8.2),
type="l", col="red")
## End(Not run)
Technicals
Technicals
Description
PUBLIC list: a collection programming-technical constants
Value
A list with elements:
Haccur
Hstart
maxiter
accuracy for iterative (Follows2006) pH calculations (max. deviation in [H+])
start [H+] for an iterative pH calculation
maximum number of iterations for iterative (Follows2006) pH calculation method
as well as for the application of the standard R function uniroot
unirootinterval
the interval (in terms of [H+]) for pH calculation using the standard R function
uniroot
uniroottol
the interval (in terms of [H+]) for pH calculation using the standard R function
uniroot
epsilon_fraction
fraction of disturbance for the numerical calculation of derivatives of TA with
respect to changes in the dissociation constants
revelle_fraction
fraction of disturbance for the numerical calculation of the revelle factor
CO2
fugacity of CO2 in atm
48
titration
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
titration
titration
Description
PUBLIC function: creates an object of class aquaenv which contains a titration simulation
Usage
titration(aquaenv, mass_sample, mass_titrant, conc_titrant,
S_titrant=NULL, steps, type="HCl", seawater_titrant=FALSE,
k_w=NULL, k_co2=NULL, k_hco3=NULL, k_boh3=NULL, k_hso4=NULL,
k_hf=NULL, k1k2="lueker", khf="dickson")
Arguments
aquaenv
an object of type aquaenv: minimal definition, contains all information about
the system: T, S, d, total concentrations of nutrients etc (Note that it is possible
to give values for SumBOH4, SumHSO4, and SumHF in the sample other than
the ones calculated from salinity)
mass_sample
the mass of the sample solution in kg
mass_titrant
the total mass of the added titrant solution in kg
conc_titrant
the concentration of the titrant solution in mol/kg-soln
S_titrant
the salinity of the titrant solution, if not supplied it is assumed that the titrant
solution has the same salinity as the sample solution
steps
the amount of steps the mass of titrant is added in
type
the type of titrant: either "HCl" or "NaOH", default: "HCl"
seawater_titrant
is the titrant based on natural seawater? (does it contain SumBOH4, SumHSO4,
and SumHF in the same proportions as seawater, i.e., correlated to S?); Note that
you can only assume a seawater based titrant (i.e. SumBOH4, SumHSO4, and
SumHF ~ S) or a water based titrant (i.e. SumBOH4, SumHSO4, and SumHF
= 0). It is not possible to give values for SumBOH4, SumHSO4, and SumHF of
the titrant.
k_w
a fixed K\_W can be specified
k_co2
a fixed K\_CO2 can be specified; used for TA fitting: give a K\_CO2 and NOT
calculate it from T and S: i.e. K\_CO2 can be fitted in the routine as well
k_hco3
a fixed K\_HCO3 can be specified
k_boh3
a fixed K\_BOH3 can be specified
k_hso4
a fixed K\_HSO4 can be specified
titration
49
k_hf
a fixed K\_HF can be specified
k1k2
either "lueker" (default, Lueker2000) or "roy" (Roy1993a) for K\_CO2 and
K\_HCO3.
khf
either "dickson" (default, Dickson1979a) or "perez" (Perez1987a) for K\_HF
Value
object of class aquaenv which contains a titration simulation
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
Examples
## Not run:
####################
# Titration with HCl
####################
S <- 35
t <- 15
SumCO2 <- 0.003500
SumNH4 <- 0.000020
mass_sample <- 0.01 # the mass of the sample solution in kg
mass_titrant <- 0.02 # the total mass of the added titrant solution in
# kg
conc_titrant <- 0.01 # the concentration of the titrant solution in
# mol/kg-soln
S_titrant
<- 0.5 # the salinity of the titrant solution (the
# salinity of a solution with a ionic strength of
# 0.01 according to: I = (19.924 S) / (1000 - 1.005S)
steps
<- 50
# the amount of steps the mass of titrant is added
# in
type
<- "HCl"
pHstart <- 11.3
ae <- titration(aquaenv(S=S, t=t, SumCO2=SumCO2, SumNH4=SumNH4,
pH=pHstart), mass_sample, mass_titrant, conc_titrant,
S_titrant, steps, type)
# plotting everything
plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]",
mfrow=c(10,10))
# plotting selectively
size <- c(12,8) #inches
50
watdepth
mfrow <- c(4,4)
what <- c("TA", "pH", "CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH",
"NH4", "NH3", "H2SO4", "HSO4", "SO4", "HF", "F", "pCO2")
plot(ae, xval=ae$delta_mass_titrant, xlab="HCl solution added [kg]",
what=what, size=size, mfrow=mfrow)
plot(ae, xval=ae$pH, xlab="free scale pH", what=what, size=size,
mfrow=mfrow)
# different x values
plot(ae, xval=ae$delta_conc_titrant, xlab="[HCl] offset added
[mol/kg-soln]", what=what, size=size, mfrow=mfrow)
plot(ae, xval=ae$delta_moles_titrant, xlab="HCl added [mol]", what=what,
size=size, mfrow=mfrow)
# bjerrum plots
par(mfrow=c(1,1))
plot(ae, bjerrum=TRUE)
what <- c("CO2", "HCO3", "CO3")
plot(ae, what=what, bjerrum=TRUE)
plot(ae, what=what, bjerrum=TRUE, lwd=4, palette=c("cyan", "magenta",
"yellow"), bg="gray", legendinset=0.1, legendposition="topleft")
what
<- c("CO2", "HCO3", "CO3", "BOH3", "BOH4", "OH", "NH4", "NH3",
"H2SO4", "HSO4", "SO4", "HF", "F")
plot(ae, what=what, bjerrum=TRUE, log=TRUE)
plot(ae, what=what, bjerrum=TRUE, log=TRUE, ylim=c(-6,-1),
legendinset=0, lwd=3, palette=c(1,3,4,5,6,colors()[seq(100,250,6)]))
## End(Not run)
watdepth
watdepth
Description
PUBLIC function: calculates the depth (in m) from the gauge pressure p (or the total pressure P)
and the latitude (in degrees: -90 to 90) and the atmospheric pressure Pa (in bar)
Usage
watdepth(P=Pa, p=pmax(0, P-Pa), lat=0, Pa=1.013253)
watdepth
51
Arguments
P
total pressure in bar, standard: 1 atm (at the sea surface)
p
gauge pressure in bar (total pressure minus atmospheric pressure), standard: 0
(at the water surface)
lat
latitude in degrees: -90 to 90, standard: 0
Pa
atmospheric pressure in bar, standard: 1 atm (at sea level)
Value
water depth d in meters
Author(s)
Andreas F. Hofmann. Maintained by Karline Soetaert ([email protected]).
References
Fofonoff1983
Examples
watdepth(100)
plot(watdepth(1:100))
Index
AquaEnv (AquaEnv_package), 8
aquaenv, 2
AquaEnv_package, 8
as.data.frame.aquaenv, 10
∗Topic misc
aquaenv, 2
as.data.frame.aquaenv, 10
BufferFactors, 10
c.aquaenv, 12
ConcRelCl, 13
convert, 13
DeltaPcoeffs, 15
gauge_p, 16
K0_CO2, 16
K0_O2, 17
K_BOH3, 19
K_CO2, 20
K_H2PO4, 21
K_H2S, 22
K_H3PO4, 23
K_HCO3, 24
K_HF, 25
K_HPO4, 26
K_HSO4, 27
K_NH4, 28
K_SiOH4, 29
K_SiOOH3, 30
K_W, 31
Ksp_aragonite, 18
Ksp_calcite, 19
length.aquaenv, 32
MeanMolecularMass, 32
merge.aquaenv, 33
PhysChemConst, 33
plot.aquaenv, 34
sample_dickson1981, 39
sample_dickson2007, 40
TAfit, 40
Technicals, 47
titration, 48
watdepth, 50
∗Topic package
AquaEnv_package, 8
BufferFactors, 10
c.aquaenv, 12
ConcRelCl, 13
convert, 13
DeltaPcoeffs, 15
gauge_p, 16
K0_CO2, 16
K0_O2, 17
K_BOH3, 19
K_CO2, 20
K_H2PO4, 21
K_H2S, 22
K_H3PO4, 23
K_HCO3, 24
K_HF, 25
K_HPO4, 26
K_HSO4, 27
K_NH4, 28
K_SiOH4, 29
K_SiOOH3, 30
K_W, 31
Ksp_aragonite, 18
Ksp_calcite, 19
length.aquaenv, 32
MeanMolecularMass, 32
merge.aquaenv, 33
PhysChemConst, 33
plot.aquaenv, 34
sample_dickson1981, 39
52
INDEX
sample_dickson2007, 40
TAfit, 40
Technicals, 47
titration, 48
watdepth, 50
53